Scaling: What’s the difference between Ctrl+A and S?
CTRLA while in Edit Mode changes the vertex radius; nothing else.
Only things like modifiers that use that property of the vertex to change something are affected. It's a nondestructive and indirect way of control since it only affects functions that read that value from the vertex.
Scaling on the other hand, at least in Edit Mode actually changes the mesh. It moves stuff to or away from the current pivot point. It is direct manipulation of the mesh.